The CER confirmed it had received the payment which originally fell due in June 2013. The payment included the amount of $6.1 million, plus 20 per cent interest per annum, through to December 31, 2013.

According to the CER, the amount paid on April 1 cleared the debt as it stood at December 31, but did not include interest accrued at the rate of 20 per cent per annum since then.

A further debt in the amount of $2.27 million fell due in February 2014 at the end of the final surrender period, CER said.

Yesterday Mr Palmer told the ABC that newspaper reports suggesting the CER was preparing to shut down Queensland Nickel over the unpaid bill were false.

"The Clean Energy [Regulator] wrote to us and said we had until the 5th of April," Mr Palmer said.

"We wrote back and said we would [pay]. It's well before the due date of the 5th of April."

It is understood Queensland Nickel is continuing with a High Court challenge against the legal validity of the carbon pricing scheme.